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Consequences of Recombination on Traditional Phylogenetic Analysis
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Recombination and the power of statistical tests of neutrality
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An African HIV-1 sequence from 1959 and implications for the origin of the epidemic
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The signature of balancing selection: Fungal mating compatibility gene evolution
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The molecular clock of HIV-1 unveiled through analysis of a known transmission history
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Ancestral Inference from Samples of DNA Sequences with Recombination
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STATISTICAL PROPERTIES OF THE NUMBER OF RECOMBINATION EVENTS IN THE HISTORY OF A SAMPLE OF DNA SEQUENCES
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Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans.
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Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants
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Maximum-Likelihood Estimation of Migration Rates and Effective Population Numbers in Two Populations Using a Coalescent Approach
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The Coalescent With Gene Conversion
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Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites
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Phylogenetic evidence for recombination in dengue virus
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Recombination and the Molecular Clock
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How clonal are human mitochondria?
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African Populations and the Evolution of Human Mitochondrial DNA
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The Myth of Eve: Molecular Biology and Human Origins: F. J. Ayala
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Linkage Disequilibrium and Recombination in Hominid Mitochondrial DNA
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Evidence of Recombination among Enteroviruses
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Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences
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A pattern recognition-based approach for phylogenetic network construction with constrained recombination
inferred← citeshttps://doi.org/10.1016/j.pnpbp.2010.02.003openalex-snapshot
A genetic schizophrenia-susceptibility region located between the ANKK1 and DRD2 genes
inferred← citeshttps://doi.org/10.1016/j.sajb.2014.01.013openalex-snapshot
Genome scan of Kenyan Themeda triandra populations by AFLP markers reveals a complex genetic structure and hints for ongoing environmental selection
inferred← citeshttps://doi.org/10.1016/j.shpsc.2004.12.002openalex-snapshot
Paradigm change in evolutionary microbiology
inferred← citeshttps://doi.org/10.1016/j.sjbs.2013.09.009openalex-snapshot
Evidence of selection pressures of neuraminidase gene (NA) of influenza A virus subtype H5N1 on different hosts in Guangxi Province of China
inferred← citeshttps://doi.org/10.1016/j.syapm.2005.05.007openalex-snapshot
Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands
inferred← citeshttps://doi.org/10.1016/j.syapm.2009.01.001openalex-snapshot
Evolution of pathogenicity in the Bacillus cereus group
inferred← citeshttps://doi.org/10.1016/j.tig.2026.05.003openalex-snapshot
Phylogenomics beyond the ‘bag-of-genes’ model
inferred← citeshttps://doi.org/10.1016/j.tim.2016.09.009openalex-snapshot
Architecture of a Species: Phylogenomics of Staphylococcus aureus
inferred← citeshttps://doi.org/10.1016/j.toxicon.2015.08.009openalex-snapshot
The importance of being genomic: Non-coding and coding sequences suggest different models of toxin multi-gene family evolution
inferred← citeshttps://doi.org/10.1016/j.tpb.2017.10.008openalex-snapshot
On the joint distribution of tree height and tree length under the coalescent
inferred← citeshttps://doi.org/10.1016/j.tpb.2021.09.008openalex-snapshot
A compendium of covariances and correlation coefficients of coalescent tree properties
inferred← citeshttps://doi.org/10.1016/j.tree.2004.09.001openalex-snapshot
Eve ?n? Steve: recombination of human mitochondrial DNA
inferred← citeshttps://doi.org/10.1016/j.tree.2004.10.009openalex-snapshot
Germs, genomes and genealogies
inferred← citeshttps://doi.org/10.1016/j.tree.2025.06.011openalex-snapshot
Recombination-aware phylogenomics
inferred← citeshttps://doi.org/10.1016/j.vetmic.2013.06.010openalex-snapshot
Phylogeny, spatio-temporal phylodynamics and evolutionary scenario of Torque teno sus virus 1 (TTSuV1) and 2 (TTSuV2) in wild boars: Fast dispersal and high genetic diversity
inferred← citeshttps://doi.org/10.1016/j.vetmic.2015.10.003openalex-snapshot
Molecular and antigenic characteristics of Massachusetts genotype infectious bronchitis coronavirus in China
inferred← citeshttps://doi.org/10.1016/j.virol.2007.03.023openalex-snapshot
Recombination in feline immunodeficiency virus genomes from naturally infected cougars
inferred← citeshttps://doi.org/10.1016/j.virol.2013.11.033openalex-snapshot
Towards inferring the global movement of beak and feather disease virus
inferred← citeshttps://doi.org/10.1016/j.virol.2016.12.031openalex-snapshot
A novel pathogenic aviadenovirus from red-bellied parrots (Poicephalus rufiventris) unveils deep recombination events among avian host lineages
inferred← citeshttps://doi.org/10.1016/j.virol.2024.110173openalex-snapshot
Novel pathogenic adenovirus in Timneh grey parrot (Psittacus timneh) unveils distinct lineage within Aviadenovirus
inferred← citeshttps://doi.org/10.1016/j.virusres.2017.12.006openalex-snapshot
Direct sequencing of the white spot syndrome virus from Brazil: Genome assembly and new insights on phylogeny
inferred← citeshttps://doi.org/10.1016/j.virusres.2023.199058openalex-snapshot
Molecular evolution analysis of three species gyroviruses in China from 2018 to 2019
inferred← citeshttps://doi.org/10.1016/j.virusres.2024.199490openalex-snapshot
Comprehensive phylogenomic analysis of Zika virus: Insights into its origin, past evolutionary dynamics, and global spread
inferred← citeshttps://doi.org/10.1016/j.virusres.2024.199499openalex-snapshot
Molecular epidemiology and pathogenicity of Wesselsbron virus circulating in Africa
inferred← citeshttps://doi.org/10.1016/j.ympev.2004.03.013openalex-snapshot
Linking phylogenetics with population genetics to reconstruct the geographic origin of a species
inferred← citeshttps://doi.org/10.1016/j.ympev.2004.08.020openalex-snapshot
Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.11.023openalex-snapshot
Comparative analysis of a translocated copy of the trnK intron in carnivorous family Nepenthaceae
inferred← citeshttps://doi.org/10.1016/j.ympev.2008.08.017openalex-snapshot
An exploratory algorithm to identify intra-host recombinant viral sequences
inferred← citeshttps://doi.org/10.1016/j.ympev.2009.10.004openalex-snapshot
The hidden diversity of Coleodactylus amazonicus (Sphaerodactylinae, Gekkota) revealed by molecular data
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.11.015openalex-snapshot
Evolution and diversification within the intertidal brown macroalgae Fucus spiralis/F. vesiculosus species complex in the North Atlantic
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.06.006openalex-snapshot
Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.03.001openalex-snapshot
Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.04.024openalex-snapshot
Evolution of circoviruses in lorikeets lags behind its hosts
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.08.003openalex-snapshot
The genetic relationship between R. microplus and R. decoloratus ticks in South Africa and their population structure
inferred← citeshttps://doi.org/10.1016/s0042-6822(03)00109-0openalex-snapshot
Evidence of recombination in natural populations of hepatitis A virus
inferred← citeshttps://doi.org/10.1016/s0169-5347(00)02027-9openalex-snapshot
How does recombination affect phylogeny estimation?
inferred← citeshttps://doi.org/10.1016/s0169-5347(01)02326-6openalex-snapshot
Prospects for nuclear gene phylogeography
inferred← citeshttps://doi.org/10.1016/s0169-5347(03)00125-3openalex-snapshot
Animal mitochondrial DNA recombination revisited
inferred← citeshttps://doi.org/10.1016/s1386-6532(05)00393-8openalex-snapshot
Genetic diversity and evolution of hepatitis C virus in the Latin American region
inferred← citeshttps://doi.org/10.1016/s1567-1348(02)00036-9openalex-snapshot
Recombination in Mycoplasma hominis
inferred← citeshttps://doi.org/10.1016/s2666-5247(21)00149-xopenalex-snapshot
Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis
inferred← citeshttps://doi.org/10.1017/cbo9780511614927.002openalex-snapshot
Molecular phylogenetics for conservation biology
inferred← citeshttps://doi.org/10.1017/cbo9780511819049.016openalex-snapshot
Estimating selection pressures on alignments of coding sequences
inferred← citeshttps://doi.org/10.1017/s0016672303006128openalex-snapshot
Potential impact of recombination on sitewise approaches for detecting positive natural selection
inferred← citeshttps://doi.org/10.1017/s0016672305007317openalex-snapshot
Evolutionary history of the Drosophila bipectinata species complex
inferred← citeshttps://doi.org/10.1017/s0016672306008330openalex-snapshot
The speciation history of the Drosophila nasuta complex
inferred← citeshttps://doi.org/10.1017/s0016672309990139openalex-snapshot
Measuring the degree of starshape in genealogies – summary statistics and demographic inference
inferred← citeshttps://doi.org/10.1017/s0016672312000298openalex-snapshot
Impact of fertility transmission and other sociodemographic factors on reproductive success and coalescent trees
inferred← citeshttps://doi.org/10.1017/s1464793101005668openalex-snapshot
On the origin and evolution of the human immunodeficiency virus (HIV)
inferred← citeshttps://doi.org/10.1034/j.1601-5223.2002.1360302.xopenalex-snapshot
Genetic diversity and the phylogeography of parthenogenesis: comparing bisexual and thelytokous populations of Nemasoma varicorne (Diplopoda: Nemasomatidae) in Denmark
inferred← citeshttps://doi.org/10.1038/35052098openalex-snapshot
Retroviral recombination: what drives the switch?
inferred← citeshttps://doi.org/10.1038/418144aopenalex-snapshot
Multiply infected spleen cells in HIV patients
inferred← citeshttps://doi.org/10.1038/hdy.2009.148openalex-snapshot
Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.)
inferred← citeshttps://doi.org/10.1038/hdy.2009.88openalex-snapshot
New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict
inferred← citeshttps://doi.org/10.1038/hdy.2010.14openalex-snapshot
Don't forget the ancestral polymorphisms
inferred← citeshttps://doi.org/10.1038/hdy.2012.22openalex-snapshot
Genetic diversity of MHC class I loci in six non-model frogs is shaped by positive selection and gene duplication
inferred← citeshttps://doi.org/10.1038/hdy.2013.101openalex-snapshot
Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation
inferred← citeshttps://doi.org/10.1038/hdy.2016.54openalex-snapshot
Genome-wide SNP data suggest complex ancestry of sympatric North Pacific killer whale ecotypes
inferred← citeshttps://doi.org/10.1038/ismej.2015.149openalex-snapshot
Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections
inferred← citeshttps://doi.org/10.1038/nature22401openalex-snapshot
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
inferred← citeshttps://doi.org/10.1038/npre.2008.2123.1openalex-snapshot
An ancient adaptive episode of convergent molecular evolution confounds phylogenetic inference
inferred← citeshttps://doi.org/10.1038/nrg3226openalex-snapshot
Transforming clinical microbiology with bacterial genome sequencing
inferred← citeshttps://doi.org/10.1038/nrg964openalex-snapshot
The evolutionary genomics of pathogen recombination
inferred← citeshttps://doi.org/10.1038/s41467-024-47464-5openalex-snapshot
Data-driven recombination detection in viral genomes
inferred← citeshttps://doi.org/10.1038/s41467-025-65286-xopenalex-snapshot
Immunological surveillance against cancer across mammals
inferred← citeshttps://doi.org/10.1038/s41559-017-0435-9openalex-snapshot
Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium
inferred← citeshttps://doi.org/10.1038/s41586-022-05189-9openalex-snapshot
Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape
inferred← citeshttps://doi.org/10.1038/s41586-025-09740-2openalex-snapshot
An ancient recombination desert is a speciation supergene in placental mammals
inferred← citeshttps://doi.org/10.1038/s41598-017-07152-5openalex-snapshot
Emergence of recombinant Mayaro virus strains from the Amazon basin
inferred← citeshttps://doi.org/10.1038/s41598-018-26596-xopenalex-snapshot
Characterization of Papaya ringspot virus isolates infecting transgenic papaya ‘Huanong No.1’ in South China
inferred← citeshttps://doi.org/10.1038/s41598-018-33049-yopenalex-snapshot
Genetic conflicts with Plasmodium parasites and functional constraints shape the evolution of erythrocyte cytoskeletal proteins
inferred← citeshttps://doi.org/10.1038/s41598-021-81622-9openalex-snapshot
Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes
inferred← citeshttps://doi.org/10.1038/sj.hdy.6800079openalex-snapshot
S-allele diversity in Sorbus aucuparia and Crataegus monogyna (Rosaceae: Maloideae)
inferred← citeshttps://doi.org/10.1038/sj.hdy.6800892openalex-snapshot
Selection and recombination drive the evolution of MHC class II DRB diversity in ungulates
inferred← citeshttps://doi.org/10.1038/srep22157openalex-snapshot
The evolutionary history of genes involved in spoken and written language: beyond FOXP2
inferred← citeshttps://doi.org/10.1046/j.1365-2540.2001.00965.xopenalex-snapshot
What do patterns of genetic variability reveal about mitochondrial recombination?
inferred← citeshttps://doi.org/10.1046/j.1365-294x.2003.01765.xopenalex-snapshot
Patterns of linkage disequilibrium in mitochondrial DNA of 16 ruminant populations
inferred← citeshttps://doi.org/10.1046/j.1365-294x.2003.01773.xopenalex-snapshot
Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects
inferred← citeshttps://doi.org/10.1073/pnas.0405667102openalex-snapshot
Discovery of a free-living chlorophyll d -producing cyanobacterium with a hybrid proteobacterial/cyanobacterial small-subunit rRNA gene
inferred← citeshttps://doi.org/10.1073/pnas.0936469100openalex-snapshot
Tracing the origin and history of the HIV-2 epidemic
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